[Bioperl-l] One to three letter code for amino acids

[Heikki Lehvaslaiho]

Jason Stajich wrote:
> 
> Somehow I really must have missed the discussion or let it slip out of
> my head... I had added the method 'valid_aa' to CodonTable a little while
> ago.  Should it be relocated to SeqUtils?

I missed that. Yes, I think SeqUtils would be a better place for valid_aa().

> In addition, I want to do the following to allow us to centralize the
> places where we keep the aa/nt codes.  Okay if I commit it?

Sure. 

Centralization is good. Should we move all alphabet related hashes there? We
could take %onecode and %threecode out of Bio::SeqUtils and but keep the
public methods. Then %onecode could be removed from CodonTable, too.

	-Heikki

> % cvs diff Bio/Tools/CodonTable.pm
> RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/CodonTable.pm,v
> retrieving revision 1.21
> diff -r1.21 CodonTable.pm
> 168a169
> > use Bio::Tools::IUPAC;
> 272,306c273,274
> < my %iupac_dna =
> <     ( 'a' => [qw( a       )],
> <       'c' => [qw( c       )],
> <       'g' => [qw( g       )],
> <       't' => [qw( t       )],
> <       'u' => [qw( t       )],
> <       'm' => [qw( a c     )],
> <       'r' => [qw( a g     )],
> <       'w' => [qw( a t     )],
> <       'k' => [qw( g t     )],
> <       'y' => [qw( c t     )],
> <       's' => [qw( c g     )],
> <       'v' => [qw( a c g   )],
> <       'h' => [qw( a c t   )],
> <       'd' => [qw( a g t   )],
> <       'b' => [qw( c g t   )],
> <       'n' => [qw( a c g t )],
> <       'x' => [qw( a c g t )],
> <      );
> <
> < my %iupac_aa =
> <     ( A => [qw(A)],      B => [qw(D N)],
> <       C => [qw(C)],      D => [qw(D)],
> <       E => [qw(E)],      F => [qw(F)],
> <       G => [qw(G)],      H => [qw(H)],
> <       I => [qw(I)],      K => [qw(K)],
> <       L => [qw(L)],      M => [qw(M)],
> <       N => [qw(N)],      P => [qw(P)],
> <       Q => [qw(Q)],      R => [qw(R)],
> <       S => [qw(S)],      T => [qw(T)],
> <       U => [qw(U)],      V => [qw(V)],
> <       W => [qw(W)],      X => [qw(X)],
> <       Y => [qw(Y)],      Z => [qw(E Q)],
> <       '*' => ['*']
> <       );
> ---
> > my %iupac_dna = Bio::Tools::IUPAC->iupac_iub();
> > my %iupac_aa = Bio::Tools::IUPAC->iupac_iup();
> 
> On Wed, 12 Dec 2001, Kris Boulez wrote:
> 
> > Quoting Heikki Lehvaslaiho (heikki@ebi.ac.uk):
> > > Kris,
> > >
> > > I brought this up a year or so ago. The consensus then was that we should
> > > not overload current interfaces but instead collect these utility functions
> > > in a separate place. I've put several, including this one, into
> > > Bio::SeqUtils.
> > >
> > Sorry didn't look close enough.
> >
> > Kris,
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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